Metadata-Version: 2.1
Name: PacbioDataProcessing
Version: 1.0.7
Summary: Tools to process PacBio sequencing data at molecule level
Keywords: PacBio,DNA,biology,sequencing,methylations
Author-email: David Palao <david.palao@gmail.com>, David Velázquez <david.velazquez@protonmail.com>
Maintainer-email: David Palao <david.palao@gmail.com>
Requires-Python: >=3.8
Description-Content-Type: text/x-rst
Classifier: Development Status :: 5 - Production/Stable
Classifier: Environment :: Console
Classifier: Intended Audience :: Science/Research
Classifier: License :: OSI Approved :: GNU General Public License v3 or later (GPLv3+)
Classifier: Natural Language :: English
Classifier: Programming Language :: Python :: 3
Classifier: Programming Language :: Python :: 3.9
Classifier: Operating System :: OS Independent
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
Requires-Dist: biopython
Requires-Dist: pysam
Requires-Dist: pyfaidx
Requires-Dist: matplotlib
Requires-Dist: seaborn~=0.12
Requires-Dist: pandas
Requires-Dist: numpy
Requires-Dist: bump2version ; extra == "dev"
Requires-Dist: flit ; extra == "dev"
Requires-Dist: watchdog ; extra == "dev"
Requires-Dist: Sphinx ; extra == "doc"
Requires-Dist: Sphinx-Substitution-Extensions ; extra == "doc"
Requires-Dist: sphinx-prompt ; extra == "doc"
Requires-Dist: Gooey ; extra == "gui"
Requires-Dist: psutil ; extra == "test"
Requires-Dist: pytest ; extra == "test"
Requires-Dist: pytest-runner ; extra == "test"
Requires-Dist: pytest-cov ; extra == "test"
Requires-Dist: pytest-subtests ; extra == "test"
Requires-Dist: flake8 ; extra == "test"
Requires-Dist: tox ; extra == "test"
Requires-Dist: coverage ; extra == "test"
Project-URL: Documentation, https://pacbio-data-processing.readthedocs.io/en/latest/
Project-URL: Source, https://gitlab.com/dvelazquez/pacbio-data-processing
Provides-Extra: dev
Provides-Extra: doc
Provides-Extra: gui
Provides-Extra: test

========
Overview
========

.. image:: https://badge.fury.io/py/PacbioDataProcessing.svg
	   :target: https://badge.fury.io/py/PacbioDataProcessing

.. image:: https://img.shields.io/pypi/pyversions/PacbioDataProcessing
	   :target: https://pypi.python.org/pypi/PacbioDataProcessing
	   :alt: PyPI - Python Version

.. image:: https://readthedocs.org/projects/pacbio-data-processing/badge/?version=latest
           :target: https://pacbio-data-processing.readthedocs.io/en/latest/?badge=latest
	   :alt: Documentation Status


This project is about detecting modifications of DNA in PacBio
sequencing data stored in the BAM format.
The PacBio sequencing data is processed at molecule level: each molecule/ZMW/hole number
is analyzed individually.

To learn how to start using this software, have a look at the quickstart_
section.

Or check the usage_ section, for more details.


* Free software: GNU General Public License v3
* Documentation: https://pacbio-data-processing.readthedocs.io


Features
========

* Detection of individual ``m6A`` modifications in each molecule.
* The single molecule analysis of a BAM file can be performed with a command line
  interface (CLI) program ``sm-analysis`` or using a simple graphical user interface
  (GUI) program, ``sm-analysis-gui``.
* The single molecule analysis can be parallelized to speed up the processing of
  large BAM files.
* An auxiliary executable, ``bam-filter``, is also provided.


Credits
=======

This package was created with Cookiecutter_ and the `palao/cookiecutter-genrepo-pypackage`_ project template.

.. _quickstart: https://pacbio-data-processing.readthedocs.io/en/latest/quickstart.html
.. _usage: https://pacbio-data-processing.readthedocs.io/en/latest/usage/index.html
.. _Cookiecutter: https://github.com/audreyr/cookiecutter
.. _`palao/cookiecutter-genrepo-pypackage`: https://github.com/palao/cookiecutter-genrepo-pypackage

